diff --git a/src/hooks/comment-checker/cli-runner.ts b/src/hooks/comment-checker/cli-runner.ts
index 8721836e..b546125f 100644
--- a/src/hooks/comment-checker/cli-runner.ts
+++ b/src/hooks/comment-checker/cli-runner.ts
@@ -58,6 +58,45 @@ export async function processWithCli(
   }
 }
 
+export interface ApplyPatchEdit {
+  filePath: string
+  before: string
+  after: string
+}
+
+export async function processApplyPatchEditsWithCli(
+  sessionID: string,
+  edits: ApplyPatchEdit[],
+  output: { output: string },
+  cliPath: string,
+  customPrompt: string | undefined,
+  debugLog: (...args: unknown[]) => void,
+): Promise<void> {
+  debugLog("processing apply_patch edits:", edits.length)
+
+  for (const edit of edits) {
+    const hookInput: HookInput = {
+      session_id: sessionID,
+      tool_name: "Edit",
+      transcript_path: "",
+      cwd: process.cwd(),
+      hook_event_name: "PostToolUse",
+      tool_input: {
+        file_path: edit.filePath,
+        old_string: edit.before,
+        new_string: edit.after,
+      },
+    }
+
+    const result = await runCommentChecker(hookInput, cliPath, customPrompt)
+
+    if (result.hasComments && result.message) {
+      debugLog("CLI detected comments for apply_patch file:", edit.filePath)
+      output.output += `\n\n${result.message}`
+    }
+  }
+}
+
 export function isCliPathUsable(cliPath: string | null): cliPath is string {
   return Boolean(cliPath && existsSync(cliPath))
 }
diff --git a/src/hooks/comment-checker/hook.apply-patch.test.ts b/src/hooks/comment-checker/hook.apply-patch.test.ts
new file mode 100644
index 00000000..ec1b4cd8
--- /dev/null
+++ b/src/hooks/comment-checker/hook.apply-patch.test.ts
@@ -0,0 +1,83 @@
+import { describe, it, expect, mock, beforeEach } from "bun:test"
+
+const processApplyPatchEditsWithCli = mock(async () => {})
+
+mock.module("./cli-runner", () => ({
+  initializeCommentCheckerCli: () => {},
+  getCommentCheckerCliPathPromise: () => Promise.resolve("/tmp/fake-comment-checker"),
+  isCliPathUsable: () => true,
+  processWithCli: async () => {},
+  processApplyPatchEditsWithCli,
+}))
+
+const { createCommentCheckerHooks } = await import("./hook")
+
+describe("comment-checker apply_patch integration", () => {
+  beforeEach(() => {
+    processApplyPatchEditsWithCli.mockClear()
+  })
+
+  it("runs comment checker using apply_patch metadata.files", async () => {
+    // given
+    const hooks = createCommentCheckerHooks()
+
+    const input = { tool: "apply_patch", sessionID: "ses_test", callID: "call_test" }
+    const output = {
+      title: "ok",
+      output: "Success. Updated the following files:\nM src/a.ts",
+      metadata: {
+        files: [
+          {
+            filePath: "/repo/src/a.ts",
+            before: "const a = 1\n",
+            after: "// comment\nconst a = 1\n",
+            type: "update",
+          },
+          {
+            filePath: "/repo/src/old.ts",
+            movePath: "/repo/src/new.ts",
+            before: "const b = 1\n",
+            after: "// moved comment\nconst b = 1\n",
+            type: "move",
+          },
+          {
+            filePath: "/repo/src/delete.ts",
+            before: "// deleted\n",
+            after: "",
+            type: "delete",
+          },
+        ],
+      },
+    }
+
+    // when
+    await hooks["tool.execute.after"](input, output)
+
+    // then
+    expect(processApplyPatchEditsWithCli).toHaveBeenCalledTimes(1)
+    expect(processApplyPatchEditsWithCli).toHaveBeenCalledWith(
+      "ses_test",
+      [
+        { filePath: "/repo/src/a.ts", before: "const a = 1\n", after: "// comment\nconst a = 1\n" },
+        { filePath: "/repo/src/new.ts", before: "const b = 1\n", after: "// moved comment\nconst b = 1\n" },
+      ],
+      expect.any(Object),
+      "/tmp/fake-comment-checker",
+      undefined,
+      expect.any(Function),
+    )
+  })
+
+  it("skips when apply_patch metadata.files is missing", async () => {
+    // given
+    const hooks = createCommentCheckerHooks()
+    const input = { tool: "apply_patch", sessionID: "ses_test", callID: "call_test" }
+    const output = { title: "ok", output: "ok", metadata: {} }
+
+    // when
+    await hooks["tool.execute.after"](input, output)
+
+    // then
+    expect(processApplyPatchEditsWithCli).toHaveBeenCalledTimes(0)
+  })
+})
diff --git a/src/hooks/comment-checker/hook.ts b/src/hooks/comment-checker/hook.ts
index 79d147b3..89893764 100644
--- a/src/hooks/comment-checker/hook.ts
+++ b/src/hooks/comment-checker/hook.ts
@@ -1,7 +1,15 @@
 import type { PendingCall } from "./types"
 import type { CommentCheckerConfig } from "../../config/schema"
 
-import { initializeCommentCheckerCli, getCommentCheckerCliPathPromise, isCliPathUsable, processWithCli } from "./cli-runner"
+import z from "zod"
+
+import {
+  initializeCommentCheckerCli,
+  getCommentCheckerCliPathPromise,
+  isCliPathUsable,
+  processWithCli,
+  processApplyPatchEditsWithCli,
+} from "./cli-runner"
 import { registerPendingCall, startPendingCallCleanup, takePendingCall } from "./pending-calls"
 
 import * as fs from "fs"
@@ -81,13 +89,7 @@ export function createCommentCheckerHooks(config?: CommentCheckerConfig) {
     ): Promise<void> => {
       debugLog("tool.execute.after:", { tool: input.tool, callID: input.callID })
 
-      const pendingCall = takePendingCall(input.callID)
-      if (!pendingCall) {
-        debugLog("no pendingCall found for:", input.callID)
-        return
-      }
-
-      debugLog("processing pendingCall:", pendingCall)
+      const toolLower = input.tool.toLowerCase()
 
       // Only skip if the output indicates a tool execution failure
       const outputLower = output.output.toLowerCase()
@@ -102,17 +104,75 @@ export function createCommentCheckerHooks(config?: CommentCheckerConfig) {
         return
       }
 
-      try {
-        // Wait for CLI path resolution
-        const cliPath = await getCommentCheckerCliPathPromise()
+      const ApplyPatchMetadataSchema = z.object({
+        files: z.array(
+          z.object({
+            filePath: z.string(),
+            movePath: z.string().optional(),
+            before: z.string(),
+            after: z.string(),
+            type: z.string().optional(),
+          }),
+        ),
+      })
 
+      if (toolLower === "apply_patch") {
+        const parsed = ApplyPatchMetadataSchema.safeParse(output.metadata)
+        if (!parsed.success) {
+          debugLog("apply_patch metadata schema mismatch, skipping")
+          return
+        }
+
+        const edits = parsed.data.files
+          .filter((f) => f.type !== "delete")
+          .map((f) => ({
+            filePath: f.movePath ?? f.filePath,
+            before: f.before,
+            after: f.after,
+          }))
+
+        if (edits.length === 0) {
+          debugLog("apply_patch had no editable files, skipping")
+          return
+        }
+
+        try {
+          const cliPath = await getCommentCheckerCliPathPromise()
+          if (!isCliPathUsable(cliPath)) {
+            debugLog("CLI not available, skipping comment check")
+            return
+          }
+
+          debugLog("using CLI for apply_patch:", cliPath)
+          await processApplyPatchEditsWithCli(
+            input.sessionID,
+            edits,
+            output,
+            cliPath,
+            config?.custom_prompt,
+            debugLog,
+          )
+        } catch (err) {
+          debugLog("apply_patch comment check failed:", err)
+        }
+        return
+      }
+
+      const pendingCall = takePendingCall(input.callID)
+      if (!pendingCall) {
+        debugLog("no pendingCall found for:", input.callID)
+        return
+      }
+
+      debugLog("processing pendingCall:", pendingCall)
+
+      try {
+        const cliPath = await getCommentCheckerCliPathPromise()
         if (!isCliPathUsable(cliPath)) {
-          // CLI not available - silently skip comment checking
           debugLog("CLI not available, skipping comment check")
           return
         }
 
-        // CLI mode only
         debugLog("using CLI:", cliPath)
         await processWithCli(input, pendingCall, output, cliPath, config?.custom_prompt, debugLog)
       } catch (err) {